HydroShare – A Case Study of the Application of Modern Software Engineering to a Large Distributed Federally-Funded Scientific Software Development Project

HydroShare is an online collaborative system under development to support the open sharing of hydrologic data, analytical tools, and computer models. With HydroShare, scientists can easily discover, access, and analyze hydrologic data and thereby enhance the production and reproducibility of hydrologic scientific results. HydroShare also takes advantage of emerging social media functionality to enable users to enhance information about and collaboration around hydrologic data and models. HydroShare is being developed by an interdisciplinary collaborative team of domain scientists, university software developers, and professional software engineers from ten institutions located across the United States. While the combination of non–co-located, diverse stakeholders presents communication and management challenges, the interdisciplinary nature of the team is integral to the project’s goal of improving scientific software development and capabilities in academia. This chapter describes the challenges faced and lessons learned with the development of HydroShare, as well as the approach to software development that the HydroShare team adopted on the basis of the lessons learned. The chapter closes with recommendations for the application of modern software engineering techniques to large, collaborative, scientific software development projects, similar to the National Science Foundation (NSF)–funded HydroShare, in order to promote the successful application of the approach described herein by other teams for other projects

Prostitution, Condom Use, and Invasive Squamous Cell Cervical Cancer in Thailand

Cervical cancer is probably caused by a sexually transmitted agent. A case-control study was conducted in three hospitals in Thailand to investigate further the role of male sexual behavior, particularly regarding sexual contacts with prostitutes, in the development of this disease. Data were obtained from interviews with 225 married women with invasive squamous cell cervical carcinoma and 791 hospitalized controls, all of whom reported having only one sexual partner, and from interviews with their husbands. Risk of cervical cancer was strongly related to the women's husbands having visited prostitutes without using a condom when the husbands were less than 30 years old. A strong increasing trend in risk in relation to decreasing frequency of the husbands' condom use with prostitutes was observed, and a weaker increasing trend in risk with husbands' estimated lifetime total number of visits to prostitutes was found. The average latent period between the women's likely initial exposure to a sexually transmitted oncogenic agent and her diagnosis of invasive cervical cancer was about a quarter of a century. Regular use of condoms by customers of prostitutes could reduce the number of invasive cervical cancer cases in the general population of Thailand by at least one fourth. Am J Epidemiol 1996; 143: 779-8

Effect of pre-cardiac and adult stages of Dirofilaria immitis in pulmonary disease of cats: CBC, bronchial lavage cytology, serology, radiographs, CT images, bronchial reactivity, and histopathology

AbstractA controlled, blind study was conducted to define the initial inflammatory response and lung damage associated with the death of precardiac stages of Dirofilaria immitis in cats as compared to adult heartworm infections and normal cats. Three groups of six cats each were used: UU: uninfected untreated controls; PreS I: infected with 100 D. immitis L3 by subcutaneous injection and treated topically with selamectin 32 and 2 days pre-infection and once monthly for 8 months); IU: infected with 100 D. immitis L3 and left untreated. Peripheral blood, serum, bronchial lavage, and thoracic radiographic images were collected from all cats on Days 0, 70, 110, 168, and 240. CT images were acquired on Days 0, 110, and 240. Cats were euthanized, and necropsies were conducted on Day 240 to determine the presence of heartworms. Bronchial rings were collected for in vitro reactivity. Lung, heart, brain, kidney, and liver tissues were collected for histopathology. Results were compared for changes within each group. Pearson and Spearman correlations were performed for association between histologic, radiographic, serologic, hematologic and bronchoalveolar lavage (BAL) results. Infected cats treated with selamectin did not develop radiographically evident changes throughout the study, were heartworm antibody negative, and were free of adult heartworms and worm fragments at necropsy. Histologic lung scores and CT analysis were not significantly different between PreS I cats and UU controls. Subtle alveolar myofibrosis was noted in isolated areas of several PreS I cats and an eosinophilic BAL cytology was noted on Days 75 and 120. Bronchial ring reactivity was blunted in IU cats but was normal in PreS I and UU cats. The IU cats became antibody positive, and five cats developed adult heartworms. All cats with heartworms were antigen positive at one time point; but one cat was antibody positive, antigen negative, with viable adult females at necropsy. The CT revealed early involvement of all pulmonary arteries and a random pattern of parenchymal disease with severe lesions immediately adjacent to normal areas. Analysis of CT 3D reconstruction and Hounsfield units demonstrated lung disease consistent with restrictive pulmonary fibrosis with an interstitial infiltrate, absence of air trapping, and decrease in total lung volume in Group IU as compared to Groups UU and PreS I. The clinical implications of this study are that cats pretreated with selamectin 1 month before D. immitis L3 infection did not become serologically positive and did not develop pulmonary arterial hypertrophy and myofibrosis

1971

Shop Talk by Frank Santos (page 1) You\u27ve Come a Long Way, Lawn-Mower Pusher by Alan B. Albin (2) In The Eyes of the Laymen by Eugene P. Elcik (2) The Importance of Water Management by Fred V. Grau (A-1) Automatic Irrigation Systems Integrated with Pumping Systems by Michael O. Mattwell (A-5) Installation of a Complete Water Source and Automatic System by Richard C. Blake (A-19) How the Soil Conservation Service Can Help in Golf Course Management by Christopher G. Mousitakis (A-22) Our Shrinking Environment by Haim B. Gunner (A-24) Pesticides\u27 Dilemma - Emotion vs. Science by Allen H. Morgan (A-28) Effects of Turf Grasses and Trees in Neutralizing Waste Water by William E. Sopper (A-34) Unsolved and New Problems Developing in Golf Course Management by Alexander M. Radko (A-44) Coming of the Conglomerate Director of Golf Courses by Edmund B. Ault (A-48) Aquatic Weed Control by John E. Gallagher (A-52) What Project Apollo Has Done for Golf and Golf Course Architecture by Mal Purdy (A-54) Maintenance of Grass Tennis Courts by Wayne Zoppo (A-59) Diseases of Ornametnals Growing in Turf Areas by R.E. Partyka (A-62) Control of Turf Insects by John C. Schread (A-65) Lime for Turf by Henry W. Indyk (A-68) How to Stop Guessing When You Buy Seed by Dale Kern (A-71) Broad Aspects of Turf Grass Culture Other Than Golf Courses by Geoffrey S. Cornish (A-79) Establishing and Maintaining Turf int he national Capitol Parks by Alton E. Rabbitt (A-81) Preventive Maintenance on Small One Cylinder Air Cooled Engine by F. W. Hazle (A-85) Top Fairway Mower Performance by James R. Maloney (A-95) Grinding Reel Type Mowers by Ray Christopherson (A-99

Developing Scientific Software through the Open Community Engagement Process

<p>Today's research relies on trustworthy software. Many scientists develop their own software; however, the quality of academia-developed software tends to be lower than commercially-developed software because, in academia, there are barriers to using proven software engineering methods. To help overcome these barriers, the Water Science Software Institute (WSSI) has developed a model--the Open Community Engagement Process (OCEP)--which brings software engineers and scientists together to traverse a four-step, iterative process that incorporates Agile development principles and open source mechanics. As a part of OCEP, WSSI has engaged a water science community who uses a scientist-developed, computational modeling framework originally developed in the early 1990s. Efforts to improve this software have included two hackathons. This paper compares these hackathons to determine factors that influnenced hackathon outcomes. Thorough planning with sufficient lead time before a hackathon, clarification of expectations, sufficient time for discussion of objectives and clarification of domain vocabulary, and co-location of participants were identified as key factors contributing to hackathon success.</p

Data Management Lifecycle and Software Lifecycle Management in the Context of Conducting Science

<p>This paper presents an overview of the data management lifecycle and software development lifecycles to look for ways to improve sustainable science software.</p